Large-scale identification and characterization of phenolic compounds and their marker–trait association in wheat

Euphytica ◽  
2020 ◽  
Vol 216 (8) ◽  
Author(s):  
Monica Sharma ◽  
Mohammed Saba Rahim ◽  
Pankaj Kumar ◽  
Ankita Mishra ◽  
Himanshu Sharma ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Large Scale ◽  
Trait Association ◽  
Identification And Characterization

scholarly journals Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 536 ◽  
Author(s):  
Xiaobo Zhao ◽  
Liming Gan ◽  
Caixia Yan ◽  
Chunjuan Li ◽  
Quanxi Sun ◽  
...  
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
Sequencing Data ◽  
Regulatory Processes ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Identification And Characterization ◽  
Lower Expression ◽  
Weighted Correlation

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.

scholarly journals Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

2006 ◽  
Vol 34 (14) ◽  
pp. 3917-3928 ◽  
Author(s):  
Jun-ichi Takeda ◽  
Yutaka Suzuki ◽  
Mitsuteru Nakao ◽  
Roberto A. Barrero ◽  
Kanako O. Koyanagi ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Large Scale ◽  
Human Gene ◽  
Full Length ◽  
Splicing Variants ◽  
Gene Transcripts ◽  
Identification And Characterization

scholarly journals Identification and characterization of growing large-scale en-echelon fractures in a salt mine

2013 ◽  
Vol 196 (2) ◽  
pp. 1092-1105 ◽  
Author(s):  
Samira Maghsoudi ◽  
Sebastian Hainzl ◽  
Simone Cesca ◽  
Torsten Dahm ◽  
Diethelm Kaiser
Keyword(s):  
Large Scale ◽  
Salt Mine ◽  
Identification And Characterization

scholarly journals Transferrin-a modulates hepcidin expression in zebrafish embryos

Blood ◽  
2009 ◽  
Vol 113 (12) ◽  
pp. 2843-2850 ◽  
Author(s):  
Paula G. Fraenkel ◽  
Yann Gibert ◽  
Jason L. Holzheimer ◽  
Victoria J. Lattanzi ◽  
Sarah F. Burnett ◽  
...  
Keyword(s):  
Large Scale ◽  
Critical Role ◽  
Hypochromic Anemia ◽  
Zebrafish Embryos ◽  
Genetic Screens ◽  
Hepcidin Expression ◽  
Morpholino Knockdown ◽  
Low Levels ◽  
Identification And Characterization

Abstract The iron regulatory hormone hepcidin is transcriptionally up-regulated in response to iron loading, but the mechanisms by which iron levels are sensed are not well understood. Large-scale genetic screens in the zebrafish have resulted in the identification of hypochromic anemia mutants with a range of mutations affecting conserved pathways in iron metabolism and heme synthesis. We hypothesized that transferrin plays a critical role both in iron transport and in regulating hepcidin expression in zebrafish embryos. Here we report the identification and characterization of the zebrafish hypochromic anemia mutant, gavi, which exhibits transferrin deficiency due to mutations in transferrin-a. Morpholino knockdown of transferrin-a in wild-type embryos reproduced the anemia phenotype and decreased somite and terminal gut iron staining, while coinjection of transferrin-a cRNA partially restored these defects. Embryos with transferrin-a or transferrin receptor 2 (TfR2) deficiency exhibited low levels of hepcidin expression, however anemia, in the absence of a defect in the transferrin pathway, failed to impair hepcidin expression. These data indicate that transferrin-a transports iron and that hepcidin expression is regulated by a transferrin-a–dependent pathway in the zebrafish embryo.

scholarly journals Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

2018 ◽  
Author(s):  
Elsie C. Jacobson ◽  
Ralph S. Grand ◽  
Jo K. Perry ◽  
Mark H. Vickers ◽  
Ada L. Olins ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Myeloid Leukemia ◽  
Large Scale ◽  
Rna Seq ◽  
Structural Variants ◽  
The Stability ◽  
Different Sources ◽  
Identification And Characterization

AbstractCancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used Hi-C and RNA-seq to identify and compare large SVs in HL-60 and HL-60/S4 cell lines. Comparisons with previously published karyotypes identified novel SVs in both cell lines. Hi-C was used to characterize the known expansion centered on the MYC locus. The MYC expansion was integrated into known locations in HL-60/S4, and a novel location (chr4) in HL-60. The HL-60 cell line has more within-line structural variation than the HL-60/S4 derivative cell line. Collectively we demonstrate the usefulness of Hi-C and with RNA-seq data for the identification and characterization of SVs.

scholarly journals Identification and characterization of large-scale genomic rearrangements during wheat evolution

PLoS ONE ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. e0231323 ◽  
Author(s):  
Inbar Bariah ◽  
Danielle Keidar-Friedman ◽  
Khalil Kashkush
Keyword(s):  
Large Scale ◽  
Genomic Rearrangements ◽  
Wheat Evolution ◽  
Identification And Characterization

Modeling the Effects of Dislocation-Grain Boundary Interactions in Polycrystal Plasticity: Identification and Characterization of Unit Mechanisms

2001 ◽  
Vol 677 ◽  
Author(s):  
M. de Koning ◽  
R. Miller ◽  
V.V. Bulatov ◽  
F. Abraham
Keyword(s):  
Large Scale ◽  
Line Tension ◽  
Geometrical Parameters ◽  
Embedded Atom ◽  
Polycrystal Plasticity ◽  
Key Issues ◽  
Dynamics Simulations ◽  
Identification And Characterization ◽  
Atom Potential

ABSTRACTIn this paper we focus on one of the key issues in polycrystalline plasticity: the unit mechanisms involving the interactions between dislocations and grain boundaries (GB). Using a combination of large-scale molecular dynamics simulations based on an embedded atom potential and an analysis in terms of the line-tension model we identify and characterize the geometrical parameters that govern the occurrence of slip transmission, absorption, blockage, etc. in dislocation-GB interactions. The results provide a guideline for the development of quantitative micro-constitutive equations for dislocation-GB interactions to be used in meso-scale simulations of polycrystal plasticity.

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